Activin A receptor type 1C single nucleotide polymorphisms associated with esophageal squamous cell carcinoma risk in Chinese population

Table 1 distribution of selected demographic variables and risk factors in esophageal squamous cell carcinoma case and control groups, n (%)

Variable	Case group (n = 1043)	Control group (n = 1143)	P value
Age (years), mean ± SD	63.07 ± 7.27	62.64 ± 9.90	0.252
Age (years)			0.041
≥ 63	572 (54.84)	577 (50.48)
< 63	471 (45.16)	566 (49.52)
Sex			0.903
Male	758 (72.67)	828 (72.44)
Female	285 (27.33)	315 (27.56)
Smoking status			< 0.001
Never	589 (56.47)	810 (70.87)
Ever	454 (43.53)	333 (29.13)
Alcohol consumption			< 0.001
Never	714 (68.46)	1061 (92.82)
Ever	329 (31.54)	82 (7.18)

Table 2 Primary information of five selected genotyped single nucleotide polymorphisms of Activin A receptor type 1C: rs4664229 T>C, rs4556933 G>A, rs77886248 T>A, rs77263459 T>C, rs6734630 A>G

Genotyped SNPs	rs4664229	rs4556933	rs77886248	rs77263459	rs6734630
Alleles	T>C	G>A	T>A	T>C	A>G
Chromosome	2	2	2	2	2
Gene	ACVR1C
Function	3 Prime UTR variant	Synonymous variant	Intron variant	Intron variant	3 Prime UTR Variant
Chromosome position	157530426	157587377	157565301	157621261	157528286
Regulome DB score1	4	4	7	5	7
TFBS	-	-	-	-	-
MAF in database (1000 Genomes)
Global	C = 0.1414	A = 0.4403	A = 0.0078	C = 0.1042	G = 0.1865
East Asian	C = 0.0903	A = 0.3185	A = 0.0387	C = 0.2361	G = 0.0913
MAF in control	C = 0.1050	A = 0.3027	A = 0.0325	C = 0.2482	G = 0.1050
P value for HWE test in the controls	0.2551	0.6442	0.4526	0.5386	0.2630
Genotyping method	Ligation detection reaction
Genotyping value, %	98.9	98.5	98.9	98.9	98.9

¹http://www.regulomedb.org/.

TFBS: Transcription factor binding site (http://snpinfo.niehs.nih.gov/snpinfo/snpfuc.htm); HWE: Hardy-weinberg equilibrium; SNPs: Single nucleotide polymorphisms; ACVR1C: Activin A receptor type 1C; MAF: Minor allele frequency.

Table 3 Analyses of associations between selected genotyped single nucleotide polymorphisms of activin A receptor type 1C on risk of esophageal squamous cell carcinoma

Locus	Genotype	Control	Case	Co-dominant model		Dominant model	Recessive model	Addictive model
				OR (95%CI)	P value	OR (95%CI)/P value	OR (95%CI)/P value	OR (95%CI)/P value
rs4664229	TT	908	835	1	0.311	0.894 (0.721-1.107)	1.487 (0.624-3.545)	0.928 (0.76-1.131)
	TC	221	177	0.871 (0.7-1.084)	0.216	0.303	0.37	0.456
	CC	9	12	1.45 (0.608-3.459)	0.402
rs4556933	GG	550	587	1	< 0.001	0.684 (0.577-0.811)	1.349 (1.019-1.786)	0.848 (0.743-0.969)
	GA	487	311	0.598 (0.498-0.719)	< 0.001	< 0.001	0.036	0.015
	AA	101	118	1.095 (0.819-1.463)	0.541
rs77886248	TT	1066	936	1	0.087	1.408 (1.019-1.944)	0.555 (0.05-6.126)	1.366 (0.999-1.870)
	TA	70	88	1.432 (1.034-1.983)	0.031	0.038	0.631	0.051
	AA	2	1	0.569 (0.052-6.29)	0.646
rs77263459	TT	647	593	1	0.087	0.958 (0.807-1.136)	1.169 (0.84-1.628)	0.999 (0.870-1.147)
	TC	417	354	0.926 (0.773-1.109)	0.405	0.62	0.355	0.988
	CC	74	77	1.135 (0.810-1.592)	0.462
rs6734630	AA	908	838	1	0.402	0.881 (0.711-1.092)	1.236 (0.5-3.054)	0.906 (0.743-1.105)
	GA	221	177	0.868 (0.697-1.08)	0.204	0.247	0.646	0.331
	GG	9	10	1.204 (0.487-2.977)	0.688

OR: Odds ratio.

Table 4 Stratified analyses between rs4556933 polymorphism and esophageal squamous cell carcinoma risk by sex, age, smoking status and alcohol consumption

Variables	Control/case numbers				Adjusted OR/P value (95%CI of OR)
	GG	GA	AA	GA + AA	GG	GA	AA	GA + AA	AA vs (GG + GA)
Sex
Male	399/424	351/225	74/91	425/316	1	0.587/< 0.01	1.18/0.369	0.689/0.001	1.463/0.032
						(0.464-0.742)	(0.823-1.691)	(0.555-0.855)	(1.033-2.071)
Female	151/163	136/86	27/27	163/113	1	0.57/0.02	0.898/0.718	0.624/0.005	1.156/0.614
						(0.401-0.811)	(0.502-1.607)	(0.449-0.868)	(0.658-2.032)
Age
≥ 63	290/324	241/163	45/66	286/229	1	0.588/< 0.01	1.283/0.257	0.697/0.004	1.582/0.032
						(0.449-0.769)	(0.833-1.976)	(0.543-0.893)	(1.041-2.403)
< 63	260/263	246/148	56/52	302/200	1	0.568/< 0.01	0.932/0.754	0.634/0.001	1.198/0.406
						(0.427-0.755)	(0.601-1.447)	(0.487-0.826)	(0.783-1.832)
Smoking status
Ever	151/262	152/135	29/52	181/187	1	0.485/< 0.01	1.009/0.974	0.568/0.001	1.39/0.223
						(0.344-0.683)	(0.583-1.749)	(0.412-0.782)	(0.818-2.362)
Never	399/325	335/176	72/66	407/242	1	0.645/< 0.01	1.156/0.442	0.734/0.006	1.38/0.078
						(0.509-0.817)	(0.799-1.674)	(0.59-0.914)	(0.964-1.973)
Alcohol consumption
Ever	31/190	45/92	6/38	51/130	1	0.326/< 0.01	1.019/0.969	0.407/< 0.01	1.745/0.23
						(0.192-0.552)	(0.395-2.63)	(0.246-0.674)	(0.703-4.332)
Never	519/397	442/219	95/80	537/299	1	0.646/< 0.01	1.117/0.507	0.729/0.001	1.343/0.068
						(0.524-0.797)	(0.806-1.548)	(0.601-0.885)	(0.978-1.842)

OR: Odds ratio.

Table 5 Stratified analyses between rs77886248 polymorphism and esophageal squamous cell carcinoma risk by sex, age, smoking status and alcohol consumption

Variables	Control/case numbers				Adjusted OR/P value (95%CI of OR)
	TT	TA	AA	TA + AA	TT	TA	AA	TA + AA	AA vs (TA + AA)
Sex
Male	779/680	44/64	1/1	45/65	1	1.619/0.027	1.772/0.686	1.623/0.025	1.714/0.704
						(1.057-2.482)	(0.11-28.458)	(1.063-2.476)	(0.107-27.524)
Female	287/256	26/24	1/0	27/24	1	1.024/0.937		0.979/0.942
						(0.57-1.839)	-/- (-)	(0.548-1.749)	-/- (-)
Age
≥ 63	544/509	31/49	1/1	32/50	1	1.643/0.046	1.255/0.874	1.631/0.046	1.21/0.894
						(1.009-2.675)	(0.76-20.757)	(1.009-2.639)	(0.073-20.012)
< 63	522/427	39/39	1/0	40/39	1	1.158/0.559		1.134/0.616
						(0.707-1.898)	-/- (-)	(0.694-1.853)	-/- (-)
Smoking status
Ever	314/405	18/45	0/1	18/46	1	1.954/0.035	-/- (-)	2.401/0.024	-/- (-)
						(1.049-3.642)		(1.099-3.791)
Never	752/531	52/43	2/0	54/0	1	1.164/0.483	-/- (-)	1.118/0.604	-/- (-)
						(0.762-1.778)		(0.734-1.702)
Alcohol consumption
Ever	76/294	6/28	0/0	6/28	1	1.111/0.824	-/- (-)	1.111/0.824	-/- (-)
						(0.44-2.807)		(0.44-2.807)
Never	990/642	64/60	2/1	66/61	1	1.41/0.068	0.722/0.793	1.389/0.078	0.704/0.777
						(0.975-2.038)	(0.64-8.61)	(0.964-1.999)	(0.062-7.959)

OR: Odds ratio.

Table 6 Haplotype frequencies in the case and control group, and risk of esophageal squamous cell carcinoma

Haplotypes	Case (%)	Control (%)	OR (95%CI)	P value
Trs4664229Grs4556933Trs77886248Trs77263459Ars6734630	58.7	57.4	1.053 (0.929-1.192)	0.42
Trs4664229Ars4556933Trs77886248Crs77263459Ars6734630	22.0	18.9	1.211 (1.043-1.407)	0.012
Crs4664229Grs4556933Trs77886248Trs77263459Grs6734630	7.1	6.2	1.143 (0.898-1.454)	0.278
Trs4664229Ars4556933Trs77886248Trs77263459Ars6734630	5.4	5.9	0.901 (0.695-1.167)	0.429
Trs4664229Grs4556933Ars77886248Trs77263459Ars6734630	2.8	3.2	0.861 (0.605-1.226)	0.406
Trs4664229Grs4556933Trs77886248Crs77263459Ars6734630	0.6	4.7	0.126 (0.072-0.221)	< 0.01
Crs4664229Ars4556933Trs77886248Crs77263459Grs6734630	2.1	0.8	-	-
Crs4664229Ars4556933Trs77886248Trs77263459Grs6734630	0.8	1.2	-	-
Crs4664229Grs4556933Ars77886248Trs77263459Grs6734630	0.5	1.2	-	-
Crs4664229Grs4556933Trs77886248Crs77263459Grs6734630	0.1	0.1	-	-

Table 7 Linkage disequilibrium analysis using parameter D and r²

D’/ r2	rs4556933	rs77886248	rs77263459	rs6734630
rs4664229	0.156/0.001	0.123/0.005	0.333/0.004	0.997/0.985
rs4556933	-	0.993/0.016	0.849/0.588	0.154/0.001
rs77886248	-	-	0.988/0.013	0.125/0.005
rs77263459	-	-	-	0.334/0.004

D’ > 0, r² > 0 indicated linkage disequilibrium between different gene loci.